This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Comparing proteomes provides a major challenge to sample preparation, mass spectrometry, and data analysis. Here, Multidimensional Protein Identification Technology (MudPIT) is tested in conjunction with label-free sample comparison methods. A new scoring system for identifying altered protein levels is developed.